diff --git a/align.c b/align.c
index 84ef1ef..9162fa0 100644
--- a/align.c
+++ b/align.c
@@ -292,7 +292,8 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
 	r->p = p;
 }
 
-static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *ob, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
+static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *ob, const int8_t *mat,
+						  int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
 {
 	if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
 		int i;
diff --git a/index.c b/index.c
index 1b93f00..4722089 100644
--- a/index.c
+++ b/index.c
@@ -154,7 +154,7 @@ int mm_idx_getseq2(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, u
 			if (rr != rid || rs >= en) break;
 			assert(rs >= st);
 			for (j = rs; j < re; ++j)
-				b[j - st] = 1;
+				b[j - st] = mi->R[i].score;
 		}
 	}
 	return en - st;
@@ -625,20 +625,24 @@ mm_idx_bed_t *mm_idx_bed_read_list(const mm_idx_t *mi, const char *fn, uint32_t
 	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
 		mm_idx_bed_t t;
 		char *p, *q;
-		int i, id = -1, st = -1, en = -1;
+		int i, id = -1, st = -1, en = -1, sc = -1;
 		for (p = q = str.s, i = 0;; ++p) {
 			if (*p == 0 || isspace(*p)) {
 				int32_t c = *p;
 				*p = 0;
-				if (i == 0) {
+				if (i == 0) { // chr
 					id = mm_idx_name2id(mi, q);
 					if (id < 0) break; // unknown name; TODO: throw a warning
-				} else if (i == 1) {
+				} else if (i == 1) { // start
 					st = atoi(q);
 					if (st < 0) break;
-				} else if (i == 2) {
+				} else if (i == 2) { // end
 					en = atoi(q);
 					if (en < 0) break;
+				} else if (i == 3) { // name; do nothing
+				} else if (i == 4) { // BED score
+					sc = atoi(q);
+					assert(sc >= 0 && sc <= 127);
 				} else break;
 				if (c == 0) break;
 				++i, q = p + 1;
@@ -647,7 +651,7 @@ mm_idx_bed_t *mm_idx_bed_read_list(const mm_idx_t *mi, const char *fn, uint32_t
 		if (en < 0) en = st + 1;
 		if (st < 0 || st >= en) continue;
 		if (m == n) EXPAND(r, m);
-		t.x = (uint64_t)id << 32 | st, t.end = en, t.idx = -1;
+		t.x = (uint64_t)id << 32 | st, t.end = en, t.score = sc >= 0? sc : 0, t.idx = -1;
 		r[n++] = t;
 	}
 	ks_destroy(ks);
diff --git a/minimap.h b/minimap.h
index 231a9cf..9bc889e 100644
--- a/minimap.h
+++ b/minimap.h
@@ -62,6 +62,7 @@ typedef struct {
 typedef struct {
 	uint64_t x;
 	int32_t end, idx;
+	int32_t score; // NB: wasting 4 bytes due to memory alignment
 } mm_idx_bed_t;
 
 typedef struct {